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BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data
Lao H Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg, Carsten Peterson
Genome Biol. 2002; 3(8): software0003.1–software0003.6. Published online 2002 July 15.
PMCID:
PMC139402
Abstract Full Text PDF–548K Supplementary Material
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 Is Cited by the Following 74 Articles in this Archive:
CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data
Toni U. Wagner, Andreas Fischer, Eva C. Thoma, Manfred Schartl
PLoS One. 2011; 6(12): e28990. Published online 2011 December 12. doi: 10.1371/journal.pone.0028990
PMCID:
PMC3236239
Abstract Full Text PDF–517K
Breast tumors from CHEK2 1100delC-mutation carriers: genomic landscape and clinical implications
Taru A Muranen, Dario Greco, Rainer Fagerholm, Outi Kilpivaara, Kati Kämpjärvi, Kristiina Aittomäki, Carl Blomqvist, Päivi Heikkilä, Åke Borg, Heli Nevanlinna
Breast Cancer Res. 2011; 13(5): R90. Published online 2011 September 20. doi: 10.1186/bcr3015
PMCID:
PMC3262202
Abstract Full Text PDF–440K Supplementary Material
Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival
Hebert Echenique-Rivera, Alessandro Muzzi, Elena Del Tordello, Kate L. Seib, Patrice Francois, Rino Rappuoli, Mariagrazia Pizza, Davide Serruto
PLoS Pathog. 2011 May; 7(5): e1002027. Published online 2011 May 5. doi: 10.1371/journal.ppat.1002027
PMCID:
PMC3088726
Abstract Full Text PDF–2.3M Supplementary Material
Molecular Characterization of Acquired Tolerance of Tumor Cells to Picropodophyllin (PPP)
Jamileh Hashemi, Claire Worrall, Daiana Vasilcanu, Mårten Fryknäs, Luqman Sulaiman, Mohsen Karimi, Wen-Hui Weng, Weng-Onn Lui, Christina Rudduck, Magnus Axelson, Helena Jernberg-Wiklund, Leonard Girnita, Olle Larsson, Catharina Larsson
PLoS One. 2011; 6(3): e14757. Published online 2011 March 14. doi: 10.1371/journal.pone.0014757
PMCID:
PMC3056661
Abstract Full Text PDF–2.2M Supplementary Material
Comparative transcriptional profiling of the limbal epithelial crypt demonstrates its putative stem cell niche characteristics
Bina B Kulkarni, Patrick J Tighe, Imran Mohammed, Aaron M Yeung, Desmond G Powe, Andrew Hopkinson, Vijay A Shanmuganathan, Harminder S Dua
BMC Genomics. 2010; 11: 526. Published online 2010 September 29. doi: 10.1186/1471-2164-11-526
PMCID:
PMC2997017
Abstract Full Text PDF–2.9M
Transcriptional Response of Leptospira interrogans to Iron Limitation and Characterization of a PerR Homolog
Miranda Lo, Gerald L. Murray, Chen Ai Khoo, David A. Haake, Richard L. Zuerner, Ben Adler
Infect Immun. 2010 November; 78(11): 4850–4859. Published online 2010 August 30. doi: 10.1128/IAI.00435-10
PMCID:
PMC2976334
Abstract Full Text PDF–585K Supplementary Material
Detecting microRNA activity from gene expression data
Stephen F Madden, Susan B Carpenter, Ian B Jeffery, Harry Björkbacka, Katherine A Fitzgerald, Luke A O'Neill, Desmond G Higgins
BMC Bioinformatics. 2010; 11: 257. Published online 2010 May 18. doi: 10.1186/1471-2105-11-257
PMCID:
PMC2885376
Abstract Full Text PDF–1.1M Supplementary Material
Tasquinimod (ABR-215050), a quinoline-3-carboxamide anti-angiogenic agent, modulates the expression of thrombospondin-1 in human prostate tumors
Anders Olsson, Anders Björk, Johan Vallon-Christersson, John T Isaacs, Tomas Leanderson
Mol Cancer. 2010; 9: 107. Published online 2010 May 17. doi: 10.1186/1476-4598-9-107
PMCID:
PMC2885345
Abstract Full Text PDF–1022K Supplementary Material
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
Morris A Swertz, K Joeri van der Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, members of the Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Ritsert C Jansen
Genome Biol. 2010; 11(3): R27. Published online 2010 March 9. doi: 10.1186/gb-2010-11-3-r27
PMCID:
PMC2864567
Abstract Full Text PDF–2.1M
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis
Gernot Stocker, Maria Fischer, Dietmar Rieder, Gabriela Bindea, Simon Kainz, Michael Oberstolz, James G McNally, Zlatko Trajanoski
BMC Bioinformatics. 2009; 10: 390. Published online 2009 November 26. doi: 10.1186/1471-2105-10-390
PMCID:
PMC2789074
Abstract Full Text PDF–1.1M Supplementary Material
Potential predictive markers of chemotherapy resistance in stage III ovarian serous carcinomas
Lovisa Österberg, Kristina Levan, Karolina Partheen, Ulla Delle, Björn Olsson, Karin Sundfeldt, György Horvath
BMC Cancer. 2009; 9: 368. Published online 2009 October 18. doi: 10.1186/1471-2407-9-368
PMCID:
PMC2770569
Abstract Full Text PDF–1.4M Supplementary Material
Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution
Lucia Carbone, R. Alan Harris, Gery M. Vessere, Alan R. Mootnick, Sean Humphray, Jane Rogers, Sung K. Kim, Jeffrey D. Wall, David Martin, Jerzy Jurka, Aleksandar Milosavljevic, Pieter J. de Jong
PLoS Genet. 2009 June; 5(6): e1000538. Published online 2009 June 26. doi: 10.1371/journal.pgen.1000538
PMCID:
PMC2695003
Abstract Full Text PDF–834K Supplementary Material
Gene expression profiling predicts a three-gene expression signature of endometrial adenocarcinoma in a rat model
Sandra Karlsson, Björn Olsson, Karin Klinga-Levan
Cancer Cell Int. 2009; 9: 12. Published online 2009 May 8. doi: 10.1186/1475-2867-9-12
PMCID:
PMC2687412
Abstract Full Text PDF–658K Supplementary Material
Two-Step Assembly Dynamics of the Bacillus subtilis Divisome
Pamela Gamba, Jan-Willem Veening, Nigel J. Saunders, Leendert W. Hamoen, Richard A. Daniel
J Bacteriol. 2009 July; 191(13): 4186–4194. Published online 2009 May 8. doi: 10.1128/JB.01758-08
PMCID:
PMC2698510
Abstract Full Text PDF–1.2M Supplementary Material
SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data
Adriane Menßen, Götz Edinger, Joachim R Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, Gerd-R Burmester, Thomas Häupl
BMC Genomics. 2009; 10: 98. Published online 2009 March 5. doi: 10.1186/1471-2164-10-98
PMCID:
PMC2657156
Abstract Full Text PDF–3.2M
Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae
Julien Gouré, Wendy A Findlay, Vincent Deslandes, Anne Bouevitch, Simon J Foote, Janet I MacInnes, James W Coulton, John HE Nash, Mario Jacques
BMC Genomics. 2009; 10: 88. Published online 2009 February 24. doi: 10.1186/1471-2164-10-88
PMCID:
PMC2653537
Abstract Full Text PDF–1.5M Supplementary Material
EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data
Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann
BMC Bioinformatics. 2009; 10: 50. Published online 2009 February 6. doi: 10.1186/1471-2105-10-50
PMCID:
PMC2645365
Abstract Full Text PDF–2.3M
Lamin B1 controls oxidative stress responses via Oct-1
Ashraf N. Malhas, Chiu Fan Lee, David J. Vaux
J Cell Biol. 2009 January 12; 184(1): 45–55. doi: 10.1083/jcb.200804155
PMCID:
PMC2615091
Abstract Full Text PDF–1.4M Supplementary Material
Transgenic increases in seed oil content are associated with the differential expression of novel Brassica-specific transcripts
Nirmala Sharma, Maureen Anderson, Arvind Kumar, Yan Zhang, E Michael Giblin, Suzanne R Abrams, L Irina Zaharia, David C Taylor, Pierre R Fobert
BMC Genomics. 2008; 9: 619. Published online 2008 December 19. doi: 10.1186/1471-2164-9-619
PMCID:
PMC2627897
Abstract Full Text PDF–1.2M Supplementary Material
Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites
Valérie Borde, Nicolas Robine, Waka Lin, Sandrine Bonfils, Vincent Géli, Alain Nicolas
EMBO J. 2009 January 21; 28(2): 99–111. Published online 2008 December 11. doi: 10.1038/emboj.2008.257
PMCID:
PMC2634730
Full Text PDF–615K Supplementary Material
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets
Patrick J Killion, Vishwanath R Iyer
Genome Biol. 2008; 9(11): R159. Published online 2008 November 12. doi: 10.1186/gb-2008-9-11-r159
PMCID:
PMC2614491
Abstract Full Text PDF–4.8M
Two Homologous Agr-Like Quorum-Sensing Systems Cooperatively Control Adherence, Cell Morphology, and Cell Viability Properties in Lactobacillus plantarum WCFS1
Toshio Fujii, Colin Ingham, Jiro Nakayama, Marke Beerthuyzen, Ryoko Kunuki, Douwe Molenaar, Mark Sturme, Elaine Vaughan, Michiel Kleerebezem, Willem de Vos
J Bacteriol. 2008 December; 190(23): 7655–7665. Published online 2008 September 19. doi: 10.1128/JB.01489-07
PMCID:
PMC2583610
Abstract Full Text PDF–900K
MiMiR – an integrated platform for microarray data sharing, mining and analysis
Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman, Laurence Game
BMC Bioinformatics. 2008; 9: 379. Published online 2008 September 18. doi: 10.1186/1471-2105-9-379
PMCID:
PMC2572073
Abstract Full Text PDF–1.1M Supplementary Material
Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer
Elin Karlsson, Ulla Delle, Anna Danielsson, Björn Olsson, Frida Abel, Per Karlsson, Khalil Helou
BMC Cancer. 2008; 8: 254. Published online 2008 September 8. doi: 10.1186/1471-2407-8-254
PMCID:
PMC2559847
Abstract Full Text PDF–1.8M Supplementary Material
Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni
Eduardo N Taboada, Joanne M MacKinnon, Christian C Luebbert, Victor PJ Gannon, John HE Nash, Kris Rahn
BMC Evol Biol. 2008; 8: 229. Published online 2008 August 8. doi: 10.1186/1471-2148-8-229
PMCID:
PMC2527321
Abstract Full Text PDF–1.0M Supplementary Material
Molecular and cellular signatures of human vaccine adjuvants
F. Mosca, E. Tritto, A. Muzzi, E. Monaci, F. Bagnoli, C. Iavarone, D. O'Hagan, R. Rappuoli, E. De Gregorio
Proc Natl Acad Sci U S A. 2008 July 29; 105(30): 10501–10506. Published online 2008 July 23. doi: 10.1073/pnas.0804699105
PMCID:
PMC2483233
Abstract Full Text PDF–914K Supplementary Material
Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs
Sara Brommesson, Göran Jönsson, Carina Strand, Dorthe Grabau, Per Malmström, Markus Ringnér, Mårten Fernö, Ingrid Hedenfalk
BMC Clin Pathol. 2008; 8: 6. Published online 2008 July 10. doi: 10.1186/1472-6890-8-6
PMCID:
PMC2474633
Abstract Full Text PDF–1.6M Supplementary Material
Recurrent and multiple bladder tumors show conserved expression profiles
David Lindgren, Sigurdur Gudjonsson, Kowan Ja Jee, Fredrik Liedberg, Sonja Aits, Anna Andersson, Gunilla Chebil, Åke Borg, Sakari Knuutila, Thoas Fioretos, Wiking Månsson, Mattias Höglund
BMC Cancer. 2008; 8: 183. Published online 2008 June 30. doi: 10.1186/1471-2407-8-183
PMCID:
PMC2483988
Abstract Full Text PDF–480K
The CD44+/CD24- phenotype is enriched in basal-like breast tumors
Gabriella Honeth, Pär-Ola Bendahl, Markus Ringnér, Lao H Saal, Sofia K Gruvberger-Saal, Kristina Lövgren, Dorthe Grabau, Mårten Fernö, Åke Borg, Cecilia Hegardt
Breast Cancer Res. 2008; 10(3): R53. Published online 2008 June 17. doi: 10.1186/bcr2108
PMCID:
PMC2481503
Abstract Full Text PDF–502K
Isolation of an embryogenic line from non-embryogenic Brassica napus cv. Westar through microspore embryogenesis
Meghna R. Malik, Feng Wang, Joan M. Dirpaul, Ning Zhou, Joe Hammerlindl, Wilf Keller, Suzanne R. Abrams, Alison M. R. Ferrie, Joan E. Krochko
J Exp Bot. 2008 July; 59(10): 2857–2873. Published online 2008 June 13. doi: 10.1093/jxb/ern149
PMCID:
PMC2486481
Abstract Full Text PDF–832K Supplementary Material
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